Java Package for Heparan Sulfate Characterization

Overview

This repository contains the Java implementation and R-integration workflow for the characterization of complex biochemical mixtures consisting of linear chains, e.g. Heparan Sulfate (HS).

This work reproduces the mathematical modeling described in: > “Combining measurements to estimate properties and characterization extent of complex biochemical mixtures; applications to Heparan Sulfate.” > Scientific Reports 6, 24829 (2016). DOI: 10.1038/srep24829

Quick Links

🚀 Project Documentation & Figures: The primary landing page for model overviews and figure reproductions.
📚 API Reference (Javadoc): Detailed technical documentation of the Java classes and methods.

Getting Started

Prerequisites

Java JDK 11 or higher
R (with rJava, ggplot2, and patchwork packages)
Maven (for building from source)

Installation

Clone the repository and build the JAR with dependencies:

git clone [https://github.com/JoelRMath/heparan-sulfate.git](https://github.com/JoelRMath/heparan-sulfate.git)
cd heparan-sulfate
mvn clean package
The resulting JAR will be located in the target/ directory and can be called directly from R as demonstrated in the Figure Examples.